Task 10 Lab Journal (MSUD)
The structure 2BFF was analyzed with the WEBnm@ server. In one run, only chain A (alpha chain, BCKDHA) was selected, in a second run both chains (A and B) that are present in the structure were selected.
For a comparative analysis a second structure was given to the server, derived from 2BFF by removing the ligand (deleting all HETATM lines), because there is no structure without ligand for our protein.
As is described on the page of task 10, ElNémo only recognizes ATOM entries. So, we have modified the PDB structure of BCKDHA. We have replaced HETATM to ATOM and insert 2 white spaces after the keyword, because PDB entries are really sensitive to column position. Water molecules in the crystal structure may affect the result of normal mode identification. They are also removed from the structure.